Elemental sulfur-driven autotrophic denitrification process for effective removal of nitrate in mariculture wastewater: Performance, kinetics and microbial community

To date, there is a lack of systematic investigation on the elemental sulfur-driven autotrophic denitrification (SDAD) process for removing nitrate (NO3--N) from mariculture wastewater deficient in organic carbon sources. Therefore, a packed-bed reactor was established and continuously operated for 230 days to investigate the operation performance, kinetic characteristics and microbial community of SDAD biofilm process. Results indicate that the NO3--N removal efficiencies and rates varied with the operational conditions including HRT (1-4 h), influent concentrations of NO3--N (25-100 mg L-1) and DO (0.2-7.0 mg L-1), and temperature (10oC-30 °C), in the ranges of 51.4%-98.6% and 0.054-0.546 g L-1 d-1, respectively. Limestone could partially neutralize the produced acidity. Small portions of NO3--N were converted to nitrite (<4.5%) and ammonia (<2.8%) in the reactor. Operational conditions also influenced the production of acidity, nitrite and ammonia as well as sulfate. Shortening HRT and increasing influent NO3--N concentration turned the optimal fitting model depicting the NO3--N removal along the reactor from half-order to zero-order. Furthermore, the NO3--N removal was accelerated by a higher temperature and influent NO3--N concentration and a lower HRT and influent DO concentration. Microbial richness, evenness and diversity gradually decreased during the autotrophic denitrifier enrichment cultivation and the reactor start-up and operation. Sulfurimonas constituted the predominate genus and the primary functional bacteria in the reactor. This study highlights the SDAD as a promising way to control the coastal eutrophication associated with mariculture wastewater discharge.

Nitrogen and sulfur cycling driven by Campylobacterota in the sediment-water interface of deep-sea cold seep: a case in the South China Sea

Chemoautotrophs within Campylobacterota, especially Sulfurovum and Sulfurimonas, are abundant in the seawater-sediment interface of the Formosa cold seep in the South China Sea. However, the in situ activity and function of Campylobacterota are unknown. In this study, the geochemical role of Campylobacterota in the Formosa cold seep was investigated with multiple means. Two members of Sulfurovum and Sulfurimonas were isolated for the first time from deep-sea cold seep. These isolates are new chemoautotrophic species that can use molecular hydrogen as an energy source and CO2 as a sole carbon source. Comparative genomics identified an important hydrogen-oxidizing cluster in Sulfurovum and Sulfurimonas. Metatranscriptomic analysis detected high expression of hydrogen-oxidizing gene in the RS, suggesting that H2 was likely an energy source in the cold seep. Genomic analysis indicated that the Sulfurovum and Sulfurimonas isolates possess a truncated sulfur-oxidizing system, and metatranscriptomic analysis revealed that Sulfurovum and Sulfurimonas with this genotype were active in the surface of RS and likely contributed to thiosulfate production. Furthermore, geochemical and in situ analyses revealed sharply decreased nitrate concentration in the sediment-water interface due to microbial consumption. Consistently, the denitrification genes of Sulfurimonas and Sulfurovum were highly expressed, suggesting an important contribution of these bacteria to nitrogen cycling. Overall, this study demonstrated that Campylobacterota played a significant role in the cycling of nitrogen and sulfur in a deep-sea cold seep. IMPORTANCE Chemoautotrophs within Campylobacterota, in particular Sulfurovum and Sulfurimonas, are ubiquitous in deep-sea cold seeps and hydrothermal vents. However, to date, no Sulfurovum or Sulfurimonas has been isolated from cold seeps, and the ecological roles of these bacteria in cold seeps remain to be investigated. In this study, we obtained two isolates of Sulfurovum and Sulfurimonas from Formosa cold seep, South China Sea. Comparative genomics, metatranscriptomics, geochemical analysis, and in situ experimental study indicated collectively that Campylobacterota played a significant part in nitrogen and sulfur cycling in cold seep and was the cause of thiosulfate accumulation and sharp reduction of nitrate level in the sediment-water interface. The findings of this study promoted our understanding of the in situ function and ecological role of deep-sea Campylobacterota.

Sulfurimonas aquatica sp. nov., a sulfur-oxidizing bacterium isolated from water of a brackish lake

A novel chemolithoautotrophic bacterium, strain H1576^T, was isolated from water of a brackish lake. Strain H1576^T grew aerobically on inorganic sulfur compounds. Hydrogen gas did not support autotrophic growth, and heterotrophic growth was not observed. Cells were rod shaped, motile, 1.5-2.7 μm in length and 0.6-0.7 μm in width. Growth was observed at 3-22 °C with an optimum growth temperature of 13-15 °C. The pH range for growth was 6.0-7.4 with an optimum pH of 6.6-6.8. Major fatty acids were summed feature 3 (C_{16: 1}ω7c and/or C_{16: 1}ω6c). The complete genome of strain H1576^T consists of a circular chromosome and a plasmid, with total length of 2.8 Mbp and G+C content of 46.4 mol%. Phylogenetic analyses indicated that strain H1576^T belongs to the genus Sulfurimonas but distinct from representatives of existing species. On the basis of genomic and phenotypic characteristics, a new species named Sulfurimonas aquatica sp. nov. is proposed with the type strain of strain H1576^T (= BCRC 81254^T = JCM 35004^T).

The Eastern Nebraska Salt Marsh Microbiome Is Well Adapted to an Alkaline and Extreme Saline Environment

The Eastern Nebraska Salt Marshes contain a unique, alkaline, and saline wetland area that is a remnant of prehistoric oceans that once covered this area. The microbial composition of these salt marshes, identified by metagenomic sequencing, appears to be different from well-studied coastal salt marshes as it contains bacterial genera that have only been found in cold-adapted, alkaline, saline environments. For example, Rubribacterium was only isolated before from an Eastern Siberian soda lake, but appears to be one of the most abundant bacteria present at the time of sampling of the Eastern Nebraska Salt Marshes. Further enrichment, followed by genome sequencing and metagenomic binning, revealed the presence of several halophilic, alkalophilic bacteria that play important roles in sulfur and carbon cycling, as well as in nitrogen fixation within this ecosystem. Photosynthetic sulfur bacteria, belonging to Prosthecochloris and Marichromatium, and chemotrophic sulfur bacteria of the genera Sulfurimonas, Arcobacter, and Thiomicrospira produce valuable oxidized sulfur compounds for algal and plant growth, while alkaliphilic, sulfur-reducing bacteria belonging to Sulfurospirillum help balance the sulfur cycle. This metagenome-based study provides a baseline to understand the complex, but balanced, syntrophic microbial interactions that occur in this unique inland salt marsh environment.

Simultaneous removal of ammonium from landfill leachate and hydrogen sulfide from biogas using a novel two-stage oxic-anoxic system

Anoxic biodesulfurization has been achieved in several bioreactor systems that have shown robustness and high elimination capacities (ECs). However, the high operating costs of this technology, which are mainly caused by the high requirements of nitrite or nitrate, make its full-scale application difficult. In the present study, the use of biologically produced nitrate/nitrite by nitrification of two different ammonium substrates, namely synthetic medium and landfill leachate, is proposed as a novel alternative. The results demonstrate the feasibility of using both ammonium substrates as nutrient solutions. A maximum elemental sulfur production of 95 ± 1% and a maximum H₂S EC of 141.18 g S-H₂S m^-3 h^-1 (RE = 95.0%) was obtained using landfill leachate as the ammonium source. Next Generation Sequencing (NGS) analysis of the microbial community revealed that the most common genera present in the desulfurizing bioreactor were Sulfurimonas (91.8-50.9%) followed by Thauera (1.1-24.2%) and Lentimicrobium (2.0-9.7%).

Candidatus Sulfurimonas marisnigri sp. nov. and Candidatus Sulfurimonas baltica sp. nov., thiotrophic manganese oxide reducing chemolithoautotrophs of the class Campylobacteria isolated from the pelagic redoxclines of the Black Sea and the Baltic Sea

Species of the genus Sulfurimonas are reported and isolated from terrestrial habitats and marine sediments and water columns with steep redox gradients. Here we report on the isolation of strains SoZ1 and GD2 from the pelagic redoxcline of the Black Sea and the Baltic Sea, respectively. Both strains are gram-stain-negative and appear as short and slightly curved motile rods. The autecological preferences for growth of strain SoZ1 were 0-25°C (optimum 20°C), pH 6.5-9.0 (optimum pH 7.5-8.0) and salinity 10-40gL^-1 (optimum 25gL^-1). Preferences for growth of strain GD2 were 0-20°C (optimum 15°C), pH 7.0-8.0 (optimum pH 7.0-7.5) and salinity 5-40gL^-1 (optimum 21gL^-1). Strain SoZ1 grew chemolithoautotrophically, while strain GD2 also showed heterotrophic growth with short chained fatty acids as carbon source. Both species utilized hydrogen (H₂), sulfide (H₂S here taken as the sum of H₂S, HS^- and S^2-), elemental sulfur (S⁰) and thiosulfate (S₂O₃^2-) as electron donors and nitrate (NO₃^-), oxygen (O₂) and particulate manganese oxide (MnO₂) as electron acceptors. Based on 16S rRNA gene sequence similarity, both strains cluster within the genus Sulfurimonas with Sulfurimonas gotlandica GD1^T as the closest cultured relative species with a sequence similarity of 96.74% and 96.41% for strain SoZ1 and strain GD2, respectively. Strains SoZ1 and GD2 share a ribosomal 16S sequence similarity of 99.27% and were demarcated based on average nucleotide identity and average amino acid identity of the whole genome sequence. These calculations have been applied to the whole genus. We propose the names Candidatus Sulfurimonas marisnigri sp. nov. and Candidatus Sulfurimonas baltica sp. nov. for the thiotrophic manganese reducing culture isolates from the Black Sea and Baltic Sea, respectively.

A bacterial isolate from the Black Sea oxidizes sulfide with manganese(IV) oxide

Mn is one of the most abundant redox-sensitive metals on earth. Some microorganisms are known to use Mn(IV) oxide (MnO₂) as electron acceptor for the oxidation of organic compounds or hydrogen (H₂), but so far the use of sulfide (H₂S) has been suggested but not proven. Here we report on a bacterial isolate which grows autotrophically and couples the reduction of MnO₂ to the oxidation of H₂S or thiosulfate (S₂O₃²⁻) for energy generation. The isolate, originating from the Black Sea, is a species within the genus Sulfurimonas, which typically occurs with high cell numbers in the vicinity of sulfidic environments [Y. Han, M. Perner, Front. Microbiol. 6, 989 (2015)]. H₂S and S₂O₃²⁻ are oxidized completely to sulfate (SO₄²⁻) without the accumulation of intermediates. In the culture, Mn(IV) reduction proceeds via Mn(III) and finally precipitation of Ca-rich Mn(II) carbonate [Mn(Ca)CO₃]. In contrast to Mn-reducing bacteria, which use organic electron donors or H₂, Fe oxides are not observed to support growth, which may either indicate an incomplete gene set or a different pathway for extracellular electron transfer.

Broad Phylogenetic Diversity Associated with Nitrogen Loss through Sulfur Oxidation in a Large Public Marine Aquarium

Denitrification by sulfur-oxidizing bacteria is an effective nitrate removal strategy in engineered aquatic systems. However, the community taxonomic and metabolic diversity of sulfur-driven denitrification (SDN) systems, as well as the relationship between nitrate removal and SDN community structure, remains underexplored. This is particularly true for SDN reactors applied to marine aquaria, despite the increasing use of this technology to supplement filtration. We applied 16S rRNA gene, metagenomic, and metatranscriptomic analyses to explore the microbial basis of SDN reactors operating on Georgia Aquarium's Ocean Voyager, the largest indoor closed-system seawater exhibit in the United States. The exhibit's two SDN systems vary in water retention time and nitrate removal efficiency. The systems also support significantly different microbial communities. These communities contain canonical SDN bacteria, including a strain related to Thiobacillus thioparus that dominates the system with the higher water retention time and nitrate removal but is effectively absent from the other system. Both systems contain a wide diversity of other microbes whose metagenome-assembled genomes contain genes of SDN metabolism. These include hundreds of strains of the epsilonproteobacterium Sulfurimonas, as well as gammaproteobacterial sulfur oxidizers of the Thiotrichales and Chromatiales, and a relative of Sedimenticola thiotaurini with complete denitrification potential. The SDN genes are transcribed and the taxonomic richness of the transcript pool varies markedly among the enzymatic steps, with some steps dominated by transcripts from noncanonical SDN taxa. These results indicate complex and variable SDN communities that may involve chemical dependencies among taxa as well as the potential for altering community structure to optimize nitrate removal.IMPORTANCE Engineered aquatic systems such as aquaria and aquaculture facilities have large societal value. Ensuring the health of animals in these systems requires understanding how microorganisms contribute to chemical cycling and waste removal. Focusing on the largest seawater aquarium in the United States, we explore the microbial communities in specialized reactors designed to remove excess nitrogen through the metabolic activity of sulfur-consuming microbes. We show that the diversity of microbes in these reactors is both high and highly variable, with distinct community types associated with significant differences in nitrogen removal rate. We also show that the genes encoding the metabolic steps of nitrogen removal are distributed broadly throughout community members, suggesting that the chemical transformations in this system are likely a result of microbes relying on other microbes. These results provide a framework for future studies exploring the contributions of different community members, both in waste removal and in structuring microbial biodiversity.

Low Light Availability Alters Root Exudation and Reduces Putative Beneficial Microorganisms in Seagrass Roots

Seagrass roots host a diverse microbiome that is critical for plant growth and health. Composition of microbial communities can be regulated in part by root exudates, but the specifics of these interactions in seagrass rhizospheres are still largely unknown. As light availability controls primary productivity, reduced light may impact root exudation and consequently the composition of the root microbiome. Hence, we analyzed the influence of light availability on root exudation and community structure of the root microbiome of three co-occurring seagrass species, Halophila ovalis, Halodule uninervis and Cymodocea serrulata. Plants were grown under four light treatments in mesocosms for 2 weeks; control (100% surface irradiance (SI), medium (40% SI), low (20% SI) and fluctuating light (10 days 20% and 4 days 100%). 16S rDNA amplicon sequencing revealed that microbial diversity, composition and predicted function were strongly influenced by the presence of seagrass roots, such that root microbiomes were unique to each seagrass species. Reduced light availability altered seagrass root exudation, as characterized using fluorescence spectroscopy, and altered the composition of seagrass root microbiomes with a reduction in abundance of potentially beneficial microorganisms. Overall, this study highlights the potential for above-ground light reduction to invoke a cascade of changes from alterations in root exudation to a reduction in putative beneficial microorganisms and, ultimately, confirms the importance of the seagrass root environment - a critical, but often overlooked space.

Diversity of Total Bacterial Communities and Chemoautotrophic Populations in Sulfur-Rich Sediments of Shallow-Water Hydrothermal Vents off Kueishan Island, Taiwan

Shallow-water hydrothermal vents (HTVs) are an ecologically important habitat with a geographic origin similar to that of deep-sea HTVs. Studies on shallow-water HTVs have not only facilitated understanding of the influences of vents on local ecosystems but also helped to extend the knowledge on deep-sea vents. In this study, the diversity of bacterial communities in the sediments of shallow-water HTVs off Kueishan Island, Taiwan, was investigated by examining the 16S ribosomal RNA gene as well as key functional genes involved in chemoautotrophic carbon fixation (aclB, cbbL and cbbM). In the vent area, Sulfurovum and Sulfurimonas of Epsilonproteobacteria appeared to dominate the benthic bacterial community. Results of aclB gene analysis also suggested involvement of these bacteria in carbon fixation using the reductive tricarboxylic acid (rTCA) cycle. Analysis of the cbbM gene showed that Alphaproteobacterial members such as the purple non-sulfur bacteria were the major chemoautotrophic bacteria involving in carbon fixation via the Calvin-Benson-Bassham (CBB) cycle. However, they only accounted for <2% of the total bacterial community in the vent area. These findings suggest that the rTCA cycle is the major chemoautotrophic carbon fixation pathway in sediments of the shallow-water HTVs off Kueishan Island.

The globally widespread genus Sulfurimonas: versatile energy metabolisms and adaptations to redox clines

Sulfurimonas species are commonly isolated from sulfidic habitats and numerous 16S rRNA sequences related to Sulfurimonas species have been identified in chemically distinct environments, such as hydrothermal deep-sea vents, marine sediments, the ocean's water column, and terrestrial habitats. In some of these habitats, Sulfurimonas have been demonstrated to play an important role in chemoautotrophic processes. Sulfurimonas species can grow with a variety of electron donors and acceptors, which may contribute to their widespread distribution. Multiple copies of one type of enzyme (e.g., sulfide:quinone reductases and hydrogenases) may play a pivotal role in Sulfurimonas' flexibility to colonize disparate environments. Many of these genes appear to have been acquired through horizontal gene transfer which has promoted adaptations to the distinct habitats. Here we summarize Sulfurimonas' versatile energy metabolisms and link their physiological properties to their global distribution.

Microbial diversity in shallow-water hydrothermal sediments of Kueishan Island, Taiwan as revealed by pyrosequencing

Kueishan Island is a young volcanic island in the southernmost edge of the Okinawa Trough in the northeastern part of Taiwan. A cluster of hydrothermal vents is located off the southeastern tip of the Island at water depths between 10 and 80 m. This paper presents the results of the first study on the microbial communities in bottom sediments collected from the shallow-water hydrothermal vents of Kueishan Island. Small-subunit ribosomal RNA gene-based high-throughput 454 pyrosequencing was used to characterize the assemblages of bacteria, archaea, and small eukaryotes in sediment samples collected at various distances from the hydrothermal vents. Sediment from the vent area contained the highest diversity of archaea and the lowest diversity of bacteria and small eukaryotes. Epsilonproteobacteria were the most abundant group in the vent sediment, but their abundance decreased with increasing distance from the vent area. Most Epsilonproteobacteria belonged to the mesophilic chemolithoautotrophic genera Sulfurovum and Sulfurimonas. Recent reports on these two genera have come from deep-sea hydrothermal vents. Conversely, the relative contribution of Gammaproteobacteria to the bacterial community increased with increasing distance from the vent area. Our study revealed the contrasting effects of venting on the benthic bacterial and archaeal communities, and showed that the sediments of the shallow-waters hydrothermal vents were dominated by chemoautotrophic bacteria. The present work broadens our knowledge on microbial diversity in shallow-water hydrothermal vent habitats.

Pan-genome analyses identify lineage- and niche-specific markers of evolution and adaptation in Epsilonproteobacteria

The rapidly increasing availability of complete bacterial genomes has created new opportunities for reconstructing bacterial evolution, but it has also highlighted the difficulty to fully understand the genomic and functional variations occurring among different lineages. Using the class Epsilonproteobacteria as a case study, we investigated the composition, flexibility, and function of its pan-genomes. Models were constructed to extrapolate the expansion of pan-genomes at three different taxonomic levels. The results show that, for Epsilonproteobacteria the seemingly large genome variations among strains of the same species are less noticeable when compared with groups at higher taxonomic ranks, indicating that genome stability is imposed by the potential existence of taxonomic boundaries. The analyses of pan-genomes has also defined a set of universally conserved core genes, based on which a phylogenetic tree was constructed to confirm that thermophilic species from deep-sea hydrothermal vents represent the most ancient lineages of Epsilonproteobacteria. Moreover, by comparing the flexible genome of a chemoautotrophic deep-sea vent species to (1) genomes of species belonging to the same genus, but inhabiting different environments, and (2) genomes of other vent species, but belonging to different genera, we were able to delineate the relative importance of lineage-specific versus niche-specific genes. This result not only emphasizes the overall importance of phylogenetic proximity in shaping the variable part of the genome, but also highlights the adaptive functions of niche-specific genes. Overall, by modeling the expansion of pan-genomes and analyzing core and flexible genes, this study provides snapshots on how the complex processes of gene acquisition, conservation, and removal affect the evolution of different species, and contribute to the metabolic diversity and versatility of Epsilonproteobacteria.

Pyruvate utilization by a chemolithoautotrophic epsilonproteobacterial key player of pelagic Baltic Sea redoxclines

Pelagic redoxclines of the central Baltic Sea are dominated by the epsilonproteobacterial group Sulfurimonas GD17, considered to be the major driver of chemolithoautotrophic denitrification in this habitat. Autecological investigations of a recently isolated representative of this environmental group, Sulfurimonas gotlandica str. GD1(T), demonstrated that the bacterium grows best under sulfur-oxidizing, denitrifying conditions. However, in the presence of bicarbonate, this strain is able to use pyruvate as both an additional carbon source and an alternative electron donor. These observations suggested that the environmental group GD17 actively metabolizes organic substrates in situ. To examine this possibility, we used RNA-based stable isotope probing (RNA-SIP) on a natural redoxcline community provided with ¹³C-labeled pyruvate. While in this experiment, we were able to identify putative heterotrophic microorganisms, the uptake of ¹³C-pyruvate in GD17 nucleic acids could not be established. To resolve these contradictory findings, combined incorporation experiments with ¹⁴C- and ¹³C-labeled pyruvate were carried out in cells of strain GD1(T) cultivated under chemolithoautotrophic conditions, which favor pyruvate uptake rather than oxidation. An analysis of the labeled biomolecules revealed that pyruvate was mostly incorporated in cellular components such as amino acids, whose synthesis requires only minimal transformation. Carbon transfer into nucleic acids was not observed, explaining the inability of RNA-SIP to detect pyruvate incorporation by strain GD1(T) and the environmental group GD17. Together, these findings suggest that by integrating organic compounds such as pyruvate into cellular components S. gotlandica GD1(T) is able to replenish chemolithoautotrophic growth and thus ensure its survival in nutrient-limited habitats such as marine pelagic redoxclines.

Stimulation of autotrophic denitrification by intrusions of the bosporus plume into the anoxic black sea

Autotrophic denitrification was measured in the southwestern coastal Black Sea, where the Bosporus Plume injects oxidized chemical species (especially O₂ and NO3−) into the oxic, suboxic, and anoxic layers. Prominent oxygen intrusions caused an overlap of NOx− and sulfide at the same station where autotrophic denitrification activity was detected with incubation experiments. Several bacteria that have been proposed to oxidize sulfide in other low oxygen environments were found in the Black Sea including SUP05, Sulfurimonas, Arcobacter, and BS-GSO2. Comparison of TRFLP profiles from this mixing zone station and the Western Gyre (a station not affected by the Bosporus Plume) indicate the greatest relative abundance of Sulfurimonas and Arcobacter at the appropriate depths at the mixing zone station. The autotrophic gammaproteobacterium BS-GSO2 correlated with ammonium fluxes rather than with sulfide fluxes and the maximum in SUP05 peak height was shallower than the depths where autotrophic denitrification was detected. Notably, anammox activity was not detected at the mixing zone station, though low levels of DNA from the anammox bacteria CandidatusScalindua were present. These results provide evidence for a modified ecosystem with different N₂ production pathways in the southwest coastal region compared to that found in the rest of the Black Sea. Moreover, the same Sulfurimonas phylotype (BS139) was previously detected on >30 μm particles in the suboxic zone of the Western Gyre along with DNA of potential sulfate reducers, so it is possible that particle-attached autotrophic denitrification may be an overlooked N₂ production pathway in the central Black Sea as well.